def test_fromvcfcalldata_default(): # default array a = vcfarray.fromvcfcalldata('fixture/example-4.1.vcf') # check FORMAT fields eq_('0|0', a['NA00001']['GT'][0]) eq_(48, a['NA00001']['GQ'][0]) eq_(1, a['NA00001']['DP'][0]) eq_(51, a['NA00001']['HQ'][0][0]) eq_(51, a['NA00001']['HQ'][0][1]) # check other attributes eq_(True, a['NA00001']['called'][0]) eq_(0, a['NA00001']['gt_type'][0]) eq_(False, a['NA00001']['is_het'][0]) eq_(False, a['NA00001']['is_variant'][0])
def test_fromvcfcalldata_view2d(): # default array a = vcfarray.fromvcfcalldata('fixture/example-4.1.vcf') a = vcfarray.view2d(a).view(np.recarray) # check FORMAT fields eq_('0|0', a.GT[0,0]) eq_(48, a.GQ[0,0]) eq_(1, a.DP[0,0]) eq_(51, a.HQ[0,0][0]) eq_(51, a.HQ[0,0][1]) # check other attributes eq_(True, a.called[0,0]) eq_(0, a.gt_type[0,0]) eq_(False, a.is_het[0,0]) eq_(False, a.is_variant[0,0])
def test_fromvcfcalldata_view2d(): # default array a = vcfarray.fromvcfcalldata('fixture/example-4.1.vcf') a = vcfarray.view2d(a).view(np.recarray) # check FORMAT fields eq_('0|0', a.GT[0, 0]) eq_(48, a.GQ[0, 0]) eq_(1, a.DP[0, 0]) eq_(51, a.HQ[0, 0][0]) eq_(51, a.HQ[0, 0][1]) # check other attributes eq_(True, a.called[0, 0]) eq_(0, a.gt_type[0, 0]) eq_(False, a.is_het[0, 0]) eq_(False, a.is_variant[0, 0])